cy-root

cy-root

(Not this root)

A simple root-finding package written in Cython. Many of the implemented methods can't be found in common Python libraries.

News:

• v1.0.3: All methods now return a partially typed namedtuple-like Cython Extension object instead of namedtuple.
• v1.0.2: Vector root-finding methods can now (try to) solve systems of equations with number of inputs different from number of outputs.

Requirements

• Python 3.6+
• dynamic-default-args
• numpy
• scipy
• sympy

For compilation:

• Cython (if you want to build from .pyx files)
• A C/C++ compiler

Installation

cy-root is now available on PyPI.

pip install cy-root

Alternatively, you can build from source. Make sure you have all the dependencies installed, then clone this repo and run:

git clone git://github.com/inspiros/cy-root.git
cd cy-root
pip install .

Supported algorithms

Note: For more information about the listed algorithms, please use Google until I update the references.

Scalar root:

• Bracketing methods: (methods that require lower and upper bounds)
  • ✅ Bisect
  • ✅ Hybisect (bisection with interval analysis)
  • ✅ Regula Falsi
  • ✅ Illinois
  • ✅ Pegasus
  • ✅ Anderson–Björck
  • ✅ Dekker
  • ✅ Brent (with Inverse Quadratic Interpolation and Hyperbolic Interpolation)
  • ✅ Chandrupatla
  • ✅ Ridders
  • ✅ TOMS748
  • ✅ Wu
  • ✅ ITP
• Newton-like methods: (methods that require derivative and/or higher order derivatives)
  • ✅ Newton
  • ✅ Chebyshev
  • ✅ Halley
  • ✅ Super-Halley
  • ✅ Tangent Hyperbolas (similar to Halley)
  • ✅ Householder
• Quasi-Newton methods: (methods that approximate derivative, use interpolation, or successive iteration)
  • ✅ Secant
  • ✅ Sidi
  • ✅ Steffensen
  • ✅ Inverse Quadratic Interpolation
  • ✅ Hyperbolic Interpolation
  • ✅ Muller (for complex root)

Vector root:

• Bracketing methods: (methods that require n-dimensional bracket)
  • ✅ Vrahatis (generalized bisection using n-polygon)

• Newton-like methods: (methods that require Jacobian and/or Hessian)
  • ✅ Generalized Newton
  • ✅ Generalized Chebyshev
  • ✅ Generalized Halley
  • ✅ Generalized Super-Halley
  • ✅ Generalized Tangent Hyperbolas (similar to Generalized Halley)
• Quasi-Newton methods: (methods that approximate Jacobian, use interpolation, or successive iteration)
  • ✅ Wolfe-Bittner
  • ✅ Robinson
  • ✅ Barnes
  • ✅ Traub-Steffensen
  • ✅ Broyden (Good and Bad)
  • ✅ Klement

Derivative Approximation:

Methods that can be combined with any Newton-like root-finding methods to discard the need of analytical derivatives.

• ✅ Finite Difference (for both scalar and vector functions, up to arbitrary order)

Usage

Examples:

Example 1:

Use find_scalar_root or find_vector_root and pass method name as the first argument. This example shows the use of find_scalar_root function with itp method.

from cyroot import find_scalar_root

f = lambda x: x ** 2 - 612
result = find_scalar_root(method='itp', f=f, a=-10, b=50)
print(result)

Output:

RootResults(root=24.73863375370596, f_root=-1.1368683772161603e-13, iters=8, f_calls=10, bracket=(24.73863369031373, 24.738633753846678), f_bracket=(-3.1364744472739403e-06, 6.962181942071766e-09), precision=6.353294779160024e-08, error=1.1368683772161603e-13, converged=True, optimal=True)

The names and pointers to all implemented methods are stored in two dictionaries SCALAR_ROOT_FINDING_METHODS and VECTOR_ROOT_FINDING_METHODS.

from cyroot import SCALAR_ROOT_FINDING_METHODS, VECTOR_ROOT_FINDING_METHODS

print('scalar root methods:', SCALAR_ROOT_FINDING_METHODS.keys())
print('vector root methods:', VECTOR_ROOT_FINDING_METHODS.keys())

Example 2:

Alternatively, import the function directly. You can also see the full list of input arguments of by using help() on them.

This example shows the use of muller method for finding complex root:

from cyroot import muller

# This function has no real root
f = lambda x: x ** 4 + 4 * x ** 2 + 5
# But Muller's method can be used to find complex root
result = muller(f, x0=0, x1=10, x2=20)
print(result)

Output:

RootResults(root=(0.34356074972251255+1.4553466902253551j), f_root=(-8.881784197001252e-16-1.7763568394002505e-15j), iters=43, f_calls=43, precision=3.177770418807502e-08, error=1.9860273225978185e-15, converged=True, optimal=True)

Example 3:

Considering the parabola $f(x)=x^2-612$ in Example 1 with initial bounds $(a,b)$ where $a=-b$, many bracketing methods will fail to find a root as the values evaluated at initial bracket are identical.

In this example, we use the hybisect method which repeatedly bisects the search regions until the Bolzano criterion holds, thus can find multiple roots:

import math

from cyroot import hybisect

f = lambda x: x ** 2 - 612
# interval arithmetic function of f
interval_f = lambda x_l, x_h: ((min(abs(x_l), abs(x_h))
                                if math.copysign(1, x_l) * math.copysign(1, x_h) > 0
                                else 0) ** 2 - 612,
                               max(abs(x_l), abs(x_h)) ** 2 - 612)

result = hybisect(f, interval_f, -50, 50)
print(result)

Output:

RootResults(root=[-24.738633753707973, 24.738633753707973], f_root=[9.936229616869241e-11, 9.936229616869241e-11], split_iters=1, iters=[43, 43], f_calls=(92, 3), bracket=[(-24.738633753710815, -24.73863375370513), (24.73863375370513, 24.738633753710815)], f_bracket=[(nan, nan), (nan, nan)], precision=[5.6843418860808015e-12, 5.6843418860808015e-12], error=[9.936229616869241e-11, 9.936229616869241e-11], converged=[True, True], optimal=[True, True])

Example 4:

This example shows the use of the halley method with functions returning first and second order derivatives of f:

from cyroot import halley

f = lambda x: x ** 3 - 5 * x ** 2 + 2 * x - 1
# first order derivative
df = lambda x: 3 * x ** 2 - 10 * x + 2
# second order derivative
d2f = lambda x: 6 * x - 10

result = halley(f, df, d2f, x0=1.5)
print(result)

Output:

RootResults(root=4.613470267581537, f_root=-3.623767952376511e-13, df_root=(19.7176210537612, 17.68082160548922), iters=11, f_calls=(12, 12, 12), precision=4.9625634836147965e-05, error=3.623767952376511e-13, converged=True, optimal=True)

The householder method supports an arbitrary number of higher order derivatives:

from cyroot import householder

f = lambda x: x ** 3 - 5 * x ** 2 + 2 * x - 1
df = lambda x: 3 * x ** 2 - 10 * x + 2
d2f = lambda x: 6 * x - 10
d3f = lambda x: 6

result = householder(f, dfs=[df, d2f, d3f], x0=1.5)
print(result)  # same result

Example 5:

Similarly, to find roots of systems of equations with Newton-like methods, you have to define functions returning Jacobian (and Hessian) of F.

This example shows the use of generalized_super_halley method:

import numpy as np

from cyroot import generalized_super_halley

# all functions for vector root methods must take a numpy array
# as argument, and return an array-like object
F = lambda x: np.array([x[0] ** 2 + 2 * x[0] * np.sin(x[1]) - x[1],
                        4 * x[0] * x[1] ** 2 - x[1] ** 3 - 1])
# Jacobian
J = lambda x: np.array([
    [2 * x[0] + 2 * np.sin(x[1]), 2 * x[0] * np.cos(x[1]) - 1],
    [4 * x[1] ** 2, 8 * x[0] * x[1] - 3 * x[1] ** 2]
])
# Hessian
H = lambda x: np.array([
    [[2, 2 * np.cos(x[1])],
     [2 * np.cos(x[1]), -2 * x[0] * np.sin(x[1])]],
    [[0, 8 * x[1]],
     [8 * x[1], 8 * x[0] - 6 * x[1]]]
])

result = generalized_super_halley(F, J, H, x0=np.array([2., 2.]))
print(result)

Output: (a bit messy)

RootResults(root=array([0.48298601, 1.08951589]), f_root=array([-4.35123049e-11, -6.55444587e-11]), df_root=(array([[ 2.73877785, -0.55283751],
       [ 4.74817951,  0.6486328 ]]), array([[[ 2.        ,  0.92582907],
        [ 0.92582907, -0.85624041]],

       [[ 0.        ,  8.71612713],
        [ 8.71612713, -2.6732073 ]]])), iters=3, f_calls=(4, 4, 4), precision=0.0005808146393164461, error=6.554445874940029e-11, converged=True, optimal=True)

Example 6:

For vector bracketing root methods or vector root methods with multiple initial guesses, the input should be a 2D np.ndarray.

This example shows the use of vrahatis method (a generalized bisection) with the example function in the original paper:

import numpy as np

from cyroot import vrahatis

F = lambda x: np.array([x[0] ** 2 - 4 * x[1],
                        -2 * x[0] + x[1] ** 2 + 4 * x[1]])

# If the initial points do not form an admissible n-polygon,
# an exception will be raised.
x0s = np.array([[-2., -0.25],
                [0.5, 0.25],
                [2, -0.25],
                [0.6, 0.25]])

result = vrahatis(F, x0s=x0s)
print(result)

Output:

RootResults(root=array([4.80212874e-11, 0.00000000e+00]), f_root=array([ 2.30604404e-21, -9.60425747e-11]), iters=34, f_calls=140, bracket=array([[ 2.29193750e-10,  2.91038305e-11],
       [-6.54727619e-12,  2.91038305e-11],
       [ 4.80212874e-11,  0.00000000e+00],
       [-6.98492260e-11,  0.00000000e+00]]), f_bracket=array([[-1.16415322e-10, -3.41972179e-10],
       [-1.16415322e-10,  1.29509874e-10],
       [ 2.30604404e-21, -9.60425747e-11],
       [ 4.87891437e-21,  1.39698452e-10]]), precision=2.9904297647806717e-10, error=9.604257471622717e-11, converged=True, optimal=True)

Example 7:

This example shows the use of finite_difference to approximate derivatives when analytical solutions are not available:

import math

from cyroot import finite_difference

f = lambda x: (math.sin(x) + 1) ** x
x = 3 * math.pi / 2
d3f_x = finite_difference(f, x,
                          h=1e-4,  # step
                          order=1,  # order
                          kind='forward')  # type: forward, backward, or central
# 7.611804179666343e-36

Similarly, generalized_finite_difference can compute vector derivative of arbitrary order (order=1 for Jacobian, order=2 for Hessian), and h can be a number or a np.ndarray containing different step sizes for each dimension:

import numpy as np

from cyroot import generalized_finite_difference

F = lambda x: np.array([x[0] ** 3 - 3 * x[0] * x[1] + 5 * x[1] - 7,
                        x[0] ** 2 + x[0] * x[1] ** 2 - 4 * x[1] ** 2 + 3.5])
x = np.array([2., 3.])

# Derivatives of F will have shape (m, *([n] * order))
# where n is number of inputs, m is number of outputs
J_x = generalized_finite_difference(F, x, h=1e-4, order=1)  # Jacobian
# array([[  2.99985,  -1.00015],
#        [ 13.0003 , -11.9997 ]])
H_x = generalized_finite_difference(F, x, h=1e-3, order=2)  # Hessian
# array([[[12.   , -3.   ],
#         [-3.   ,  0.   ]],
#        [[ 2.   ,  6.001],
#         [ 6.001, -3.998]]])
K_x = generalized_finite_difference(F, x, h=1e-2, order=3)  # Kardashian, maybe
# array([[[[ 6.00000000e+00,  2.32830644e-10],
#          [ 2.32830644e-10,  2.32830644e-10]],
#         [[ 2.32830644e-10,  2.32830644e-10],
#          [ 2.32830644e-10,  1.11758709e-08]]],
#        [[[ 0.00000000e+00, -3.72529030e-09],
#          [-3.72529030e-09,  1.99999999e+00]],
#         [[-3.72529030e-09,  1.99999999e+00],
#          [ 1.99999999e+00, -1.67638063e-08]]]])

Conveniently, you can use the FiniteDifference and GeneralizedFiniteDifference classes to wrap our function and pass them to any Newton-like methods.

This is actually the default behavior when derivative functions of all Newton-like methods or the initial Jacobian guess of some vector quasi-Newton methods are not provided.

from cyroot import GeneralizedFiniteDifference, generalized_halley

J = GeneralizedFiniteDifference(F, h=1e-4, order=1)
H = GeneralizedFiniteDifference(F, h=1e-3, order=2)

result = generalized_halley(F, J=J, H=H, x0=x)
print(result)

Output:

RootResults(root=array([2.16665878, 2.11415683]), f_root=array([-5.47455414e-11,  1.05089271e-11]), df_root=(array([[ 7.74141032, -1.49997634],
       [ 8.80307666, -7.75212506]]), array([[[ 1.30059527e+01, -3.00000000e+00],
        [-3.00000000e+00, -4.54747351e-13]],

       [[ 2.00000000e+00,  4.22931366e+00],
        [ 4.22931366e+00, -3.66668244e+00]]])), iters=4, f_calls=(5, 211, 211), precision=1.0327220168881081e-07, error=5.474554143347632e-11, converged=True, optimal=True)

Output format:

The returned result is a namedtuple-like object whose elements depend on the type of the method:

• Common:
  • root: the solved root.
  • f_root: value evaluated at root.
  • iters: number of iterations.
  • f_calls: number of function calls.
  • precision: width of final bracket (for bracketing methods), or absolute difference of root with the last estimation, or the span of the set of final estimations.
  • error: absolute value of f_root.
  • converged: True if the stopping criterion is met, False if the procedure terminated prematurely.
  • optimal: True only if the error tolerance is satisfied abs(f_root) <= etol.
• Exclusive to bracketing methods:
  • bracket: final bracket.
  • f_bracket: value evaluated at final bracket.
• Exclusive to Newton-like methods:
  • df_root: derivative or tuple of derivatives (of increasing orders) evaluated at root.

Notes:

• converged can be True even if the solution is not optimal, which means the routine stopped because the precision tolerance is satisfied.
• For scipy.optimize.root users, the stopping condition arguments etol, ertol, ptol, prtol are equivalent to f_tol, f_rtol, x_tol, x_rtol, respectively (but not identical).

Configurations:

The default values for stop condition arguments (i.e. etol, ertol, ptol, prtol, max_iter) are globally set to the values defined in _defaults.py, and can be modified dynamically as follows:

import cyroot

cyroot.set_default_stop_condition_args(
    etol=1e-7,
    ptol=0,  # disable precision tolerance
    max_iter=100)

help(cyroot.illinois)  # run to check the updated docstring

For more examples, please check the examples folder.

Contributing

If you want to contribute, please contact me.
If you want an algorithm to be implemented, also drop me the paper (I will read if I have time).

License

The code is released under the MIT license. See LICENSE.txt for details.